Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 15:19:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk7_33246/04_2023/7xk7_33246_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk7_33246/04_2023/7xk7_33246.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk7_33246/04_2023/7xk7_33246_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk7_33246/04_2023/7xk7_33246_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk7_33246/04_2023/7xk7_33246_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk7_33246/04_2023/7xk7_33246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk7_33246/04_2023/7xk7_33246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk7_33246/04_2023/7xk7_33246_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk7_33246/04_2023/7xk7_33246_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.115 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 P 7 5.49 5 S 92 5.16 5 C 9830 2.51 5 N 2451 2.21 5 O 2801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "D PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 2": "OE1" <-> "OE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E ARG 100": "NH1" <-> "NH2" Residue "E PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F GLU 329": "OE1" <-> "OE2" Residue "F GLU 345": "OE1" <-> "OE2" Residue "F GLU 398": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 15186 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} Conformer: "B" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} bond proxies already assigned to first conformer: 3474 Chain: "B" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3177 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 15, 'TRANS': 396} Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1902 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "D" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1580 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1511 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 3157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3157 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 383} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 260 Unusual residues: {'FMN': 1, 'IQT': 1, 'LMT': 2, 'PEE': 2, 'RBF': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 82 Unusual residues: {' CA': 1, 'FMN': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9324 SG CYS D 112 46.524 51.343 64.710 1.00 45.30 S ATOM 10290 SG CYS E 26 44.603 55.229 65.844 1.00 41.86 S ATOM 8685 SG CYS D 29 46.490 58.333 61.442 1.00 44.16 S ATOM 11012 SG CYS E 120 48.052 54.013 59.708 1.00 45.56 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA A 338 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 338 " occ=0.50 Time building chain proxies: 10.82, per 1000 atoms: 0.71 Number of scatterers: 15186 At special positions: 0 Unit cell: (90.64, 127.6, 153.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 92 16.00 P 7 15.00 O 2801 8.00 N 2451 7.00 C 9830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.11 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 301 " pdb="FE2 FES D 301 " - pdb=" SG CYS D 29 " pdb="FE1 FES D 301 " - pdb=" SG CYS D 112 " pdb="FE2 FES D 301 " - pdb=" SG CYS E 120 " pdb="FE1 FES D 301 " - pdb=" SG CYS E 26 " pdb=" FES F 501 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 111 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 79 " Number of angles added : 9 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 79 helices and 14 sheets defined 45.1% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 171 through 184 removed outlier: 3.527A pdb=" N ALA A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 379 through 382 No H-bonds generated for 'chain 'A' and resid 379 through 382' Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 431 through 444 Processing helix chain 'B' and resid 3 through 13 removed outlier: 3.662A pdb=" N ILE B 10 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N HIS B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N HIS B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 34 removed outlier: 5.046A pdb=" N ALA B 25 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU B 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 29 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 31 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 33 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE B 34 " --> pdb=" O ALA B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 86 removed outlier: 4.131A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE B 65 " --> pdb=" O TRP B 61 " (cutoff:3.500A) Proline residue: B 66 - end of helix Processing helix chain 'B' and resid 90 through 96 Processing helix chain 'B' and resid 100 through 107 removed outlier: 3.714A pdb=" N THR B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 150 removed outlier: 3.551A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix removed outlier: 3.747A pdb=" N TRP B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 167 removed outlier: 4.163A pdb=" N ILE B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.714A pdb=" N PHE B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 removed outlier: 8.881A pdb=" N ALA B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N GLY B 247 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 277 through 289 removed outlier: 3.602A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 315 Processing helix chain 'B' and resid 321 through 324 removed outlier: 3.505A pdb=" N ASN B 324 " --> pdb=" O ALA B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 324' Processing helix chain 'B' and resid 327 through 330 No H-bonds generated for 'chain 'B' and resid 327 through 330' Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 354 through 373 removed outlier: 4.022A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 409 removed outlier: 3.920A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix removed outlier: 3.535A pdb=" N ASP B 397 " --> pdb=" O ALA B 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 32 removed outlier: 3.729A pdb=" N ILE C 25 " --> pdb=" O VAL C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 52 removed outlier: 4.075A pdb=" N ASP C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 93 through 98 removed outlier: 4.241A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 181 removed outlier: 3.536A pdb=" N GLU C 181 " --> pdb=" O GLY C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 178 through 181' Processing helix chain 'C' and resid 183 through 188 removed outlier: 3.973A pdb=" N GLN C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 removed outlier: 3.626A pdb=" N ASN C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 253 Processing helix chain 'D' and resid 6 through 16 removed outlier: 3.879A pdb=" N SER D 10 " --> pdb=" O GLU D 6 " (cutoff:3.500A) Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 20 through 23 No H-bonds generated for 'chain 'D' and resid 20 through 23' Processing helix chain 'D' and resid 28 through 33 Processing helix chain 'D' and resid 38 through 61 Processing helix chain 'D' and resid 71 through 93 removed outlier: 3.547A pdb=" N ALA D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 102 through 108 removed outlier: 4.475A pdb=" N GLY D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE D 108 " --> pdb=" O PHE D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 120 removed outlier: 3.526A pdb=" N ALA D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 124 No H-bonds generated for 'chain 'D' and resid 122 through 124' Processing helix chain 'D' and resid 127 through 157 removed outlier: 3.669A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 184 through 201 removed outlier: 4.118A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 35 through 63 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 79 through 100 Processing helix chain 'E' and resid 103 through 116 removed outlier: 5.380A pdb=" N ILE E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N PHE E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Proline residue: E 114 - end of helix Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'E' and resid 136 through 166 removed outlier: 4.154A pdb=" N LYS E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N TYR E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 5.017A pdb=" N SER E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N PHE E 193 " --> pdb=" O GLY E 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 29 removed outlier: 3.657A pdb=" N PHE F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 removed outlier: 3.726A pdb=" N GLY F 61 " --> pdb=" O THR F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 71 No H-bonds generated for 'chain 'F' and resid 69 through 71' Processing helix chain 'F' and resid 94 through 96 No H-bonds generated for 'chain 'F' and resid 94 through 96' Processing helix chain 'F' and resid 100 through 103 No H-bonds generated for 'chain 'F' and resid 100 through 103' Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 179 through 181 No H-bonds generated for 'chain 'F' and resid 179 through 181' Processing helix chain 'F' and resid 190 through 195 removed outlier: 3.722A pdb=" N LYS F 194 " --> pdb=" O GLY F 190 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 190 through 195' Processing helix chain 'F' and resid 244 through 249 removed outlier: 3.531A pdb=" N TYR F 248 " --> pdb=" O GLN F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 296 removed outlier: 3.596A pdb=" N MET F 285 " --> pdb=" O GLY F 282 " (cutoff:3.500A) Proline residue: F 287 - end of helix removed outlier: 3.791A pdb=" N HIS F 291 " --> pdb=" O MET F 288 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE F 292 " --> pdb=" O ARG F 289 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE F 293 " --> pdb=" O SER F 290 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU F 296 " --> pdb=" O PHE F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 316 No H-bonds generated for 'chain 'F' and resid 314 through 316' Processing helix chain 'F' and resid 320 through 329 Processing helix chain 'F' and resid 344 through 346 No H-bonds generated for 'chain 'F' and resid 344 through 346' Processing helix chain 'F' and resid 355 through 362 removed outlier: 3.680A pdb=" N TYR F 360 " --> pdb=" O HIS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 372 No H-bonds generated for 'chain 'F' and resid 370 through 372' Processing helix chain 'F' and resid 381 through 394 removed outlier: 3.737A pdb=" N LEU F 394 " --> pdb=" O MET F 390 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2 through 4 Processing sheet with id= B, first strand: chain 'A' and resid 28 through 32 removed outlier: 3.780A pdb=" N SER A 89 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU A 93 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL A 76 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 41 through 43 removed outlier: 6.984A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 132 through 134 removed outlier: 7.084A pdb=" N LYS A 188 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL A 151 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR A 190 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 306 through 308 removed outlier: 5.676A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N SER A 17 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N ARG A 276 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 12.744A pdb=" N VAL A 19 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.841A pdb=" N ASP C 82 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.662A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.349A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP C 129 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N THR C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 169 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N PHE C 152 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N TYR C 167 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA C 154 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU C 165 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= H, first strand: chain 'C' and resid 204 through 206 Processing sheet with id= I, first strand: chain 'F' and resid 35 through 37 removed outlier: 4.611A pdb=" N ILE F 35 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR F 49 " --> pdb=" O ILE F 35 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 80 through 82 Processing sheet with id= K, first strand: chain 'F' and resid 133 through 136 removed outlier: 4.182A pdb=" N THR F 259 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN F 169 " --> pdb=" O SER F 261 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 147 through 153 Processing sheet with id= M, first strand: chain 'F' and resid 175 through 178 Processing sheet with id= N, first strand: chain 'F' and resid 335 through 339 removed outlier: 6.281A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU F 374 " --> pdb=" O VAL F 277 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE F 279 " --> pdb=" O GLU F 374 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TYR F 376 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N GLY F 281 " --> pdb=" O TYR F 376 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N CYS F 378 " --> pdb=" O GLY F 281 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.36 Time building geometry restraints manager: 6.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.36: 4778 1.36 - 1.57: 10546 1.57 - 1.78: 15 1.78 - 1.99: 152 1.99 - 2.20: 8 Bond restraints: 15499 Sorted by residual: bond pdb=" C12 IQT B 503 " pdb=" C13 IQT B 503 " ideal model delta sigma weight residual 1.548 1.313 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" CA SER B 239 " pdb=" CB SER B 239 " ideal model delta sigma weight residual 1.534 1.403 0.130 1.45e-02 4.76e+03 8.09e+01 bond pdb=" C4A RBF B 502 " pdb=" N5 RBF B 502 " ideal model delta sigma weight residual 1.288 1.450 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" C10 RBF B 502 " pdb=" N1 RBF B 502 " ideal model delta sigma weight residual 1.304 1.461 -0.157 2.00e-02 2.50e+03 6.18e+01 bond pdb=" C5A RBF B 502 " pdb=" N5 RBF B 502 " ideal model delta sigma weight residual 1.350 1.491 -0.141 2.00e-02 2.50e+03 4.96e+01 ... (remaining 15494 not shown) Histogram of bond angle deviations from ideal: 59.41 - 77.17: 3 77.17 - 94.93: 8 94.93 - 112.68: 8520 112.68 - 130.44: 12389 130.44 - 148.20: 71 Bond angle restraints: 20991 Sorted by residual: angle pdb=" C10 IQT B 503 " pdb=" C11 IQT B 503 " pdb=" C12 IQT B 503 " ideal model delta sigma weight residual 85.87 125.44 -39.57 3.00e+00 1.11e-01 1.74e+02 angle pdb=" S1 FES F 501 " pdb="FE2 FES F 501 " pdb=" S2 FES F 501 " ideal model delta sigma weight residual 104.33 91.08 13.25 1.14e+00 7.69e-01 1.35e+02 angle pdb="FE1 FES F 501 " pdb=" S2 FES F 501 " pdb="FE2 FES F 501 " ideal model delta sigma weight residual 75.66 88.85 -13.19 1.14e+00 7.69e-01 1.34e+02 angle pdb=" S1 FES D 301 " pdb="FE2 FES D 301 " pdb=" S2 FES D 301 " ideal model delta sigma weight residual 104.33 91.43 12.90 1.14e+00 7.69e-01 1.28e+02 angle pdb="FE1 FES D 301 " pdb=" S2 FES D 301 " pdb="FE2 FES D 301 " ideal model delta sigma weight residual 75.66 88.48 -12.82 1.14e+00 7.69e-01 1.26e+02 ... (remaining 20986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 8864 35.61 - 71.22: 164 71.22 - 106.83: 13 106.83 - 142.45: 5 142.45 - 178.06: 4 Dihedral angle restraints: 9050 sinusoidal: 3609 harmonic: 5441 Sorted by residual: dihedral pdb=" CA ILE F 39 " pdb=" C ILE F 39 " pdb=" N ASN F 40 " pdb=" CA ASN F 40 " ideal model delta harmonic sigma weight residual 180.00 -145.06 -34.94 0 5.00e+00 4.00e-02 4.88e+01 dihedral pdb=" C10 FMN B 501 " pdb=" C1' FMN B 501 " pdb=" N10 FMN B 501 " pdb=" C2' FMN B 501 " ideal model delta sinusoidal sigma weight residual 257.59 79.53 178.06 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C10 FMN C 301 " pdb=" C1' FMN C 301 " pdb=" N10 FMN C 301 " pdb=" C2' FMN C 301 " ideal model delta sinusoidal sigma weight residual 257.59 86.97 170.62 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 9047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.205: 2335 0.205 - 0.410: 16 0.410 - 0.616: 3 0.616 - 0.821: 1 0.821 - 1.026: 1 Chirality restraints: 2356 Sorted by residual: chirality pdb=" C16 IQT B 503 " pdb=" C15 IQT B 503 " pdb=" C17 IQT B 503 " pdb=" O4 IQT B 503 " both_signs ideal model delta sigma weight residual True 2.43 -1.41 1.03 2.00e-01 2.50e+01 2.63e+01 chirality pdb=" CA ASP F 34 " pdb=" N ASP F 34 " pdb=" C ASP F 34 " pdb=" CB ASP F 34 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C5' LMT B 505 " pdb=" C4' LMT B 505 " pdb=" C6' LMT B 505 " pdb=" O5' LMT B 505 " both_signs ideal model delta sigma weight residual False -2.51 -1.96 -0.55 2.00e-01 2.50e+01 7.53e+00 ... (remaining 2353 not shown) Planarity restraints: 2618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 IQT B 503 " 0.215 2.00e-02 2.50e+03 1.96e-01 3.84e+02 pdb=" C13 IQT B 503 " -0.235 2.00e-02 2.50e+03 pdb=" C14 IQT B 503 " -0.150 2.00e-02 2.50e+03 pdb=" C15 IQT B 503 " 0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 IQT B 503 " 0.075 2.00e-02 2.50e+03 1.63e-01 2.67e+02 pdb=" C11 IQT B 503 " -0.206 2.00e-02 2.50e+03 pdb=" C12 IQT B 503 " 0.224 2.00e-02 2.50e+03 pdb=" C13 IQT B 503 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN C 301 " -0.069 2.00e-02 2.50e+03 2.79e-02 3.69e+01 pdb=" C10 FMN C 301 " -0.006 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " 0.023 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " -0.010 2.00e-02 2.50e+03 pdb=" C4A FMN C 301 " -0.017 2.00e-02 2.50e+03 pdb=" C5A FMN C 301 " -0.016 2.00e-02 2.50e+03 pdb=" C6 FMN C 301 " -0.015 2.00e-02 2.50e+03 pdb=" C7 FMN C 301 " 0.022 2.00e-02 2.50e+03 pdb=" C7M FMN C 301 " 0.032 2.00e-02 2.50e+03 pdb=" C8 FMN C 301 " 0.026 2.00e-02 2.50e+03 pdb=" C8M FMN C 301 " 0.017 2.00e-02 2.50e+03 pdb=" C9 FMN C 301 " -0.012 2.00e-02 2.50e+03 pdb=" C9A FMN C 301 " -0.014 2.00e-02 2.50e+03 pdb=" N1 FMN C 301 " 0.008 2.00e-02 2.50e+03 pdb=" N10 FMN C 301 " 0.002 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " 0.011 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " -0.020 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " 0.066 2.00e-02 2.50e+03 pdb=" O4 FMN C 301 " -0.029 2.00e-02 2.50e+03 ... (remaining 2615 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 106 2.56 - 3.15: 11760 3.15 - 3.73: 22131 3.73 - 4.32: 33957 4.32 - 4.90: 56346 Nonbonded interactions: 124300 Sorted by model distance: nonbonded pdb=" OD2 ASP B 397 " pdb=" O HOH B 601 " model vdw 1.978 2.440 nonbonded pdb=" OG SER B 113 " pdb=" OD1 ASP B 115 " model vdw 2.172 2.440 nonbonded pdb=" O4' FMN B 501 " pdb=" O5' FMN B 501 " model vdw 2.176 2.432 nonbonded pdb=" O HOH A 510 " pdb=" O HOH A 512 " model vdw 2.178 2.440 nonbonded pdb=" OE2 GLU F 275 " pdb=" OH TYR F 363 " model vdw 2.212 2.440 ... (remaining 124295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.240 Check model and map are aligned: 0.230 Set scattering table: 0.120 Process input model: 46.660 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.235 15499 Z= 0.549 Angle : 1.121 39.568 20991 Z= 0.619 Chirality : 0.061 1.026 2356 Planarity : 0.007 0.196 2618 Dihedral : 15.077 178.058 5580 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.51 % Favored : 97.38 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.16), residues: 1912 helix: -1.31 (0.16), residues: 853 sheet: -1.28 (0.38), residues: 149 loop : -2.00 (0.17), residues: 910 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 235 time to evaluate : 1.932 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 244 average time/residue: 1.4002 time to fit residues: 373.2322 Evaluate side-chains 172 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 168 time to evaluate : 1.851 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1321 time to fit residues: 2.5752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 96 optimal weight: 0.0170 chunk 76 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 0.0270 chunk 110 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 202 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 78 GLN B 178 GLN B 219 GLN B 240 GLN B 243 GLN B 313 ASN B 354 ASN C 37 GLN C 40 ASN C 46 GLN C 216 HIS D 18 ASN D 75 GLN D 88 GLN D 100 GLN D 176 GLN D 205 GLN E 79 ASN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 ASN F 362 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 15499 Z= 0.201 Angle : 0.569 11.622 20991 Z= 0.289 Chirality : 0.043 0.247 2356 Planarity : 0.004 0.037 2618 Dihedral : 12.480 179.153 2207 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.18), residues: 1912 helix: -0.05 (0.17), residues: 856 sheet: -0.67 (0.37), residues: 165 loop : -1.50 (0.18), residues: 891 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 179 time to evaluate : 1.843 Fit side-chains outliers start: 25 outliers final: 8 residues processed: 194 average time/residue: 1.4659 time to fit residues: 310.5827 Evaluate side-chains 169 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 161 time to evaluate : 1.796 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.2342 time to fit residues: 3.5219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 ASN E 16 ASN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.062 15499 Z= 0.640 Angle : 0.787 13.033 20991 Z= 0.394 Chirality : 0.053 0.246 2356 Planarity : 0.005 0.046 2618 Dihedral : 12.511 177.782 2207 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.33 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.18), residues: 1912 helix: -0.08 (0.17), residues: 860 sheet: -0.42 (0.41), residues: 146 loop : -1.53 (0.18), residues: 906 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 167 time to evaluate : 2.005 Fit side-chains outliers start: 44 outliers final: 23 residues processed: 199 average time/residue: 1.4583 time to fit residues: 318.0255 Evaluate side-chains 187 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 1.709 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.1498 time to fit residues: 3.2026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 15499 Z= 0.162 Angle : 0.532 11.982 20991 Z= 0.272 Chirality : 0.042 0.247 2356 Planarity : 0.004 0.039 2618 Dihedral : 11.539 176.823 2207 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.19), residues: 1912 helix: 0.53 (0.18), residues: 861 sheet: -0.24 (0.40), residues: 153 loop : -1.21 (0.19), residues: 898 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 1.862 Fit side-chains outliers start: 38 outliers final: 15 residues processed: 193 average time/residue: 1.3753 time to fit residues: 292.7507 Evaluate side-chains 172 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 157 time to evaluate : 1.839 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.2172 time to fit residues: 3.6033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 GLN D 24 GLN F 97 HIS F 362 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.058 15499 Z= 0.545 Angle : 0.716 12.663 20991 Z= 0.359 Chirality : 0.050 0.248 2356 Planarity : 0.005 0.048 2618 Dihedral : 11.751 179.086 2207 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.51 % Favored : 96.44 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.18), residues: 1912 helix: 0.31 (0.18), residues: 851 sheet: -0.23 (0.41), residues: 151 loop : -1.27 (0.19), residues: 910 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 162 time to evaluate : 1.815 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 24 residues processed: 191 average time/residue: 1.3536 time to fit residues: 285.0454 Evaluate side-chains 184 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 1.714 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 3 average time/residue: 0.1558 time to fit residues: 3.1497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 0.5980 chunk 164 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 45 optimal weight: 0.0770 chunk 182 optimal weight: 3.9990 chunk 151 optimal weight: 0.4980 chunk 84 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 15499 Z= 0.143 Angle : 0.519 11.872 20991 Z= 0.264 Chirality : 0.041 0.218 2356 Planarity : 0.004 0.038 2618 Dihedral : 10.871 176.256 2207 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.19), residues: 1912 helix: 0.80 (0.18), residues: 860 sheet: -0.12 (0.40), residues: 155 loop : -1.03 (0.19), residues: 897 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 1.758 Fit side-chains outliers start: 36 outliers final: 21 residues processed: 195 average time/residue: 1.3115 time to fit residues: 283.5089 Evaluate side-chains 177 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 156 time to evaluate : 1.810 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.2059 time to fit residues: 3.1102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 153 optimal weight: 0.3980 chunk 102 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 15499 Z= 0.252 Angle : 0.566 12.071 20991 Z= 0.285 Chirality : 0.043 0.210 2356 Planarity : 0.004 0.040 2618 Dihedral : 10.752 179.070 2207 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.19), residues: 1912 helix: 0.81 (0.18), residues: 863 sheet: -0.07 (0.40), residues: 155 loop : -0.97 (0.19), residues: 894 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 158 time to evaluate : 1.817 Fit side-chains outliers start: 32 outliers final: 24 residues processed: 182 average time/residue: 1.3661 time to fit residues: 276.4691 Evaluate side-chains 182 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 1.830 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 3 average time/residue: 0.1966 time to fit residues: 3.4636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 15499 Z= 0.185 Angle : 0.531 12.021 20991 Z= 0.268 Chirality : 0.042 0.211 2356 Planarity : 0.004 0.039 2618 Dihedral : 10.431 177.836 2207 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.19), residues: 1912 helix: 0.99 (0.18), residues: 859 sheet: 0.01 (0.41), residues: 155 loop : -0.88 (0.20), residues: 898 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 1.732 Fit side-chains outliers start: 34 outliers final: 20 residues processed: 192 average time/residue: 1.3376 time to fit residues: 284.2576 Evaluate side-chains 177 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 157 time to evaluate : 1.799 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 0.2044 time to fit residues: 3.1835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 1.9990 chunk 159 optimal weight: 0.0870 chunk 169 optimal weight: 8.9990 chunk 102 optimal weight: 0.0070 chunk 73 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 overall best weight: 2.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 15499 Z= 0.309 Angle : 0.595 12.273 20991 Z= 0.300 Chirality : 0.044 0.209 2356 Planarity : 0.004 0.040 2618 Dihedral : 10.541 179.460 2207 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.19), residues: 1912 helix: 0.82 (0.18), residues: 862 sheet: -0.30 (0.40), residues: 165 loop : -0.89 (0.20), residues: 885 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 1.783 Fit side-chains outliers start: 30 outliers final: 20 residues processed: 180 average time/residue: 1.2927 time to fit residues: 257.3357 Evaluate side-chains 172 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 1.815 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 1 average time/residue: 0.1271 time to fit residues: 2.5978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 149 optimal weight: 0.0050 chunk 15 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 15499 Z= 0.177 Angle : 0.537 11.973 20991 Z= 0.271 Chirality : 0.042 0.210 2356 Planarity : 0.004 0.042 2618 Dihedral : 10.230 177.613 2207 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.19), residues: 1912 helix: 1.07 (0.18), residues: 859 sheet: 0.04 (0.41), residues: 155 loop : -0.83 (0.20), residues: 898 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.808 Fit side-chains outliers start: 24 outliers final: 20 residues processed: 179 average time/residue: 1.3372 time to fit residues: 266.0856 Evaluate side-chains 178 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 158 time to evaluate : 1.647 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.2044 time to fit residues: 3.4133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 0.0270 chunk 138 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 chunk 131 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.137044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.103492 restraints weight = 32600.669| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.89 r_work: 0.2928 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 15499 Z= 0.181 Angle : 0.536 11.974 20991 Z= 0.270 Chirality : 0.042 0.207 2356 Planarity : 0.004 0.041 2618 Dihedral : 10.012 178.667 2207 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.19), residues: 1912 helix: 1.15 (0.18), residues: 859 sheet: -0.16 (0.40), residues: 165 loop : -0.77 (0.20), residues: 888 =============================================================================== Job complete usr+sys time: 5216.85 seconds wall clock time: 93 minutes 48.89 seconds (5628.89 seconds total)